DNA partitions into triplets under tension in the presence of organic cations, with
sequence evolutionary age predicting the stability of the triplet phase
--Manuscript
Draft--Manuscript Number: QRBP-D-17-00009
Full Title: DNA partitions into triplets under tension in the presence of organic cations, with sequence evolutionary age predicting the stability of the triplet phase
Short Title: Triplet Phase of Ancient DNA Sequences
Article Type: Report
Corresponding Author: Joshua Berryman LUXEMBOURG Corresponding Author's Institution:
First Author: Amirhossein Taghavi
Order of Authors: Amirhossein Taghavi Paul van der Schoot Joshua Berryman
Abstract: Using atomistic simulations of GC-rich DNA duplexes we show the formation of stable triplet structure when extended in solution over a timescale of hundreds of
nanoseconds, in the
presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as a solution phase of the double helix under tension, subject to the presence of stabilising co-factors. Considering the partitioning of the duplexes into triplets of base-pairs as the first step of operation of recombinase enzymes like RecA, we emphasize the structure-function relationship in Σ DNA. We supplement atomistic calculations with thermodynamic arguments to show that codons for 'phase one' amino acids (those appearing early in evolution) are more likely than a lower entropy GC-rich sequence to form triplets under tension. We further observe that the four amino acids supposed (in the 'GADV' world hypothesis) to constitute the minimal set to produce functional globular proteins have the strongest triplet-forming propensity within the phase one set, showing a series of decreasing triplet propensity with evolutionary newness.
Keywords: dna stretching; S-DNA; sigma DNA; triplet disproportionation; evolution; origin of life
Triplet phase of ancient DNA sequence 1 Title page 1 2 3 4
DNA partitions into triplets under tension in the presence of organic cations, 5
with evolutionary age predicting the stability of the triplet phase 6
7
Authors’ names: 8
9
Amirhossein Taghavi1, Paul van der Schoot2 and Joshua T. Berryman1*
10 11
1Department of Physics and Materials Science, University of Luxembourg, 162A Avenue de la 12
Faïencerie, Luxembourg City, Luxembourg 13
14
2Department of Applied Physics, Theory of Polymers and Soft matter, Technische Universiteit 15
Eindhoven P.O. Box 513 5600 MB Eindhoven 16 17 18 19 Correspondence: 20 Joshua T. Berryman, 21 22
Address : Campus Limpertsberg, Université du Luxembourg 162 A, avenue de la Faïencerie L-1511
2 1 2 3 Abstract 4
Using atomistic simulations of GC-rich DNA duplexes we show the formation of stable triplet
5
structure when extended in solution over a timescale of hundreds of nanoseconds, in the
6
presence of organic salt. We present planar-stacked triplet disproportionated DNA (Σ DNA) as
7
a solution phase of the double helix under tension, subject to the presence of stabilising
co-8
factors. Considering the partitioning of the duplexes into triplets of base-pairs as the first step
9
of operation of recombinase enzymes like RecA, we emphasize the structure-function
10
relationship in Σ DNA. We supplement atomistic calculations with thermodynamic arguments
11
to show that codons for ‘phase one’ amino acids (those appearing early in evolution) are more
12
likely than a lower entropy GC-rich sequence to form triplets under tension. We further observe
13
that the four amino acids supposed (in the ‘GADV’ world hypothesis) to constitute the minimal
14
set to produce functional globular proteins have the strongest triplet-forming propensity within
15
the phase one set, showing a series of decreasing triplet propensity with evolutionary newness.
3 INTRODUCTION
27
Under tension in aqueous solution with small or monatomic counterions, the DNA duplex
28
stretches, unwinding if not topologically constrained, and eventually denatures. The extension
29
against force shows a jump by a factor of ~1.5−1.7 (depending on sequence, pulling geometry
30
and solution) at ~ 65 pN (Williamset al., 2002; Vlassakis et al., 2008; Liu et al., 2010; Bosaeus 31
et al., 2012). Several models have been proposed to explain the sudden increase in length,
32
which is widely agreed to be the signal of a collective structural transition. The formation of
33
regions of single stranded DNA (ssDNA) (Williams et al., 2001) or of ladder-like stretched
34
and untwisted double stranded DNA (dsDNA) have been suggested (Cluzel et al., 1996;
35
Konrad and Bolonick, 1996; Lebrun and Lavery, 1996a; Smith et al., 1996). At modest
36
extensionsof sequences not dominated by AT base pairs, we expectto see a partly untwisted
37
ladder-like structure, in which the base pairs remain intact but the rise per base pair is
38
equilibrated to a new value of ~ 5.8 Å, compared to the rise in unstretched B-DNA of 3.4 Å.
39
This stretched phase or phases is known by the umbrella label of ‘S-DNA’. For
GC-40
rich structures having strong hydrogen bonding the base pairing is preserved in the S-DNA
41
structure, and the base stacking may also be somewhat preserved by tilting and sliding of the
42
base pairs or by opening of ‘bubbles’ between base-pairs. Reorientation of the base pairs
43
increases the solvent-exposed area while permitting them to remain in contact such that a
44
complete water gap does not open between them. The detailed S-DNA structure, particularly
45
the inclination, depends on the pulling scheme. When the 5´ ends of each strand are pulled, tilt
46
angle increases gradually until the terminal H-bonds are disrupted, while in the 3´3´ pulling
47
regime the tilt angle is decreased and no early breakage of H-bonds is seen (Lavery et al., 2002; 48
Li andGisler, 2009; Danilowicz et al., 2009; Bag et al., 2016).
49
The most readily available information on DNA under tension is the empirically
50
measured force-extension curve (Smith et al., 1992; Rief et al., 1999), which provides the clear
4
signal of some transition, but no atomistic-level information. This is supplemented by
52
fluorescence and polarised-light studies (Nordén et al., 1992; van Mameren et al., 2009; King 53
et al., 2013), and by atomistic simulationswhich are able to provide explicit descriptions ofthe
54
DNA but which are limited in the accessible timescalesand system sizes (Lebrun and Lavery,
55
1996b; Konrad and Bolonick, 1996; Li and Gisler, 2009). Simple energy minimisation of
56
d(GCG)4 DNA under extension (without thermal fluctuations or explicit solvent) yields
57
partition into four base-stacked triplets (Bertucat et al., 1998), however subsequent fully
58
dynamic simulations have shown instead the irregular formation of ‘denaturation bubbles’
59
(Harris et al., 2005; Rezác et al., 2010), different from the formation of regular triplets both in
60
the irregularity of the spacing and in the large disruption of base planarity and base-pairing
61
near to the solvent filled cavities formed.
62
DNA is often subjected to tension in its biological context, for purposes including
63
transport, transcription and tertiary structure manipulation (Nicklas, 1998) . A striking example
64
of this is the crystal structure (pdb: 3cmt) of DNA bound to the RecA protein (Chen et al.,
65
2008), a snapshot of the fundamental process of sexual reproduction: the recombination of
66
homologous DNA from two parent organisms. In this structure the extended protein-bound
67
DNA duplex does not adopt a recognised S-like configuration, but rather disproportionates into
68
groups of three bases, with orderly planar base stacking retained within each triplet. This triplet
69
disproportionation has been observed in solution when bound to RecA (Nordén et al.,1992), in
70
crystallogrphy structure of RecA-DNA complex (Chen et al., 2008) and also has been
71
suggested as a stable phase even without co-factors (Bosaeus et al., current work).
72
Orderly triplet formation when complexed is in contrast to current general
73
understanding of the structural behaviour when extended in solution, which leads us to examine
74
whether the triplet phase can be stabilised in solution and if it could in this case be considered
75
a canonical biologically active structure of DNA on the same footing as the A, B and Z forms.
5
Using molecular dynamics simulations of duplex DNA with an applied force, we do not
77
observe stable triplet structure in an aqueous solution of monatomic counterions, but do find
78
that it is stable without specific complex to a structured enzyme, forming triplets in a solution
79
either of terminus capped monomeric Arginine peptides (Ac-Arg+-NHMe Cl-) or (more
80
weakly) of the well-known intercalant Ethidium Bromide (Et+Br-).
81
The presence of intercalators has been observed to drive significant alterations in the 82
quasiequilibrium force vs. extension curve, with an effect at high concentrations of smoothing 83
over the B to S transition and possibly of modifying the structure of the S phase (Vladescu et 84
al., 2008). By carrying out simulated stretching experiments in the presence of DNA-binding 85
cofactors, we intend to reduce the barrier and collectivity associated 86
with the B-S transition, thus increasing the likelihood that the sub-microsecond simulation 87
timescale can describe the real (millisecond) process, and also to investigate the structural role 88
of biologically relevant moieties (Arg) in relation to DNA under tension. 89
We discuss planar-stacked triplet disproportionated DNA as a solution phase of the
90
double helix under tension, and refer to it as ‘Σ DNA’, with the three right-facing points of the
91
Σ character serving as a mnemonic for the three grouped base pairs. In the same way as for
92
unstretched Watson-Crick base paired DNA structures, we remark that the structure of the Σ
93
phase ones linked to function: the partitioning of bases into codons of three base-pairs each is
94
the first phase of operation of recombinase enzymes such as RecA, facilitating alignment of
95
homologous or near homologous sequences. By showing that this process does not require any
96
very sophisticated manipulation of the DNA, we position it as potentially appearing as an early
97
step in the development of life, and correlate the postulated sequence of incorporation of amino
98
acids (phase zero (the GADV world) (Ikehara et al., 2002), phase one and phase two (Wong,
99
1975; Wong, 2005;Koonin and Novozhilov, 2009), into molecular biology with the ease of
Σ-100
formation for sequences including the associated codons. We also note that the machinery of
6
nucleotide to peptide translation occurs necessarily with reference to triplets of bases, so that
102
further investigation into the Σ phase of single and double strands of RNA and DNA might be
103
a valuable source of insight into the origins not only of recombination, but also of gene
104 expression. 105 106 METHODS 107
Molecular structures were prepared using the Nucleic Acid Builder (NAB) (Macke and Case,
108
1998). Salt and water were represented using the Joung-Cheatham (Joung and Cheatham III,
109
2008) and TIP3P (Jorgensen et al., 1983) parameters, with the AMBER15 forcefield (Ivani et 110
al., 2015) used for DNA and the AMBER14SB forcefield used for peptides (Maier et al.,2015).
111
The Ethidium molecule was represented using the GAFF (Wang et al., 2004) with partial
112
charges and bond parameters assigned via the ANTECHAMBER tool (Wang et al., 2006).
113
Simulations were run using the GPU-accelerated implementation of pmemd (Götz et al., 2012)
114
in the AMBER16 package (Case et al., 2016). For each calculation, 16 independent replicas
115
were preparedand equilibrated in the B conformation for 10 ns. Pulling of the DNA then took
116
place using steered molecular dynamics, over a time period of 150 ns (giving a pulling rate of
117
0.68 Å ns-1). DNA was pulled using force applied to the centres of geometry of the top and
118
bottom base-pairs, such that no topological restraint was applied and force was distributed
119
equally between 3´ and 5´ strand ends. Averaging of angles (for study of DNA structural
120
parameters) was carried out by taking the mean cosine and sine, then the arctangent of the mean
121
values. Structures were analysed using CURVES+ (Lavery et al., 2009).
122
In order to present a dimensionless relative extension the unstretched contour length for
123
24 bp was estimated giving values of 3.46 Å (Arg Cl), 3.43 Å (EtBr) and 3.43 Å (NaCl) for
124
the [G12C12] sequence and 3.57 Å (Arg Cl), 3.41 Å (EtBr) and 3.38 Å (NaCl) for the
125
[(GGC)4(GAC)4].[(GTC)4(GCC)4] sequence.
7 RESULTS
127
Sequence-Dependence of Disproportionation 128
It is not clear what form the original genetic code had, as it is likely to have co-evolved to some
129
extent with the associated enzymes of transcription and translation. We can make a guess about
130
the history of the genetic code by considering the metabolic networks leading to the different
131
amino acids: it is hypothesised that a list of so-called ‘phase one’ amino acids were present
132
earlier in evolution than the ‘phase two’ amino acids, based on the complexity of the cellular
133
machinery used in current organisms to synthesize, for example, Methionine (M) from
134
Threonine (T) (Wongand Bronskill, 1979; Koonin and Novozhilov, 2009). If the genetic code
135
in the epoch of a much simplified amino-acid alphabet already had the current structure of three
136
basepairs per codon it was therefore highly redundant at this time.
137
In the current triplet code, the ‘phase one’ amino acids supposed to have been
138
incorporated earliest into biology (a list of ADEGILPSTV) are coded by triplets which have a
139
specific physical tendency: the energetic cost to break base-stacking at the triplet boundary is
140
low, relative to the complete modern genetic code. In this paper we first motivate the statistical
141
observation of preferential triplet disproportionation in the phase one genetic code. We then
142
analyse atomistic simulation data to show that disproportionation into coding triplets occurs
143
spontaneously under tension for appropriate sequences and solution conditions.
144
The weak form of our observation provides a physical mechanism to minimise
read-145
frame and recombination alignment errors in the early evolution of the genetic code. We further
146
motivate this to make the stronger claim of a possible route for the origin of the triplet genetic
147
code, with the three base-pair structure arising from simple physical conditions in the absence
148
of the sophisticated enzymatic machinery which later evolved to maintain the triplet code in
149
modern organisms with a full alphabet of amino-acids.
8
The free energy of base-stacking in duplex DNA was long ago calculated
151
combinatorically for the various pairs of bases, by Friedman and Honig (Friedman and Honig,
152
1995). Although free energy calculations for nucleic acids remain subtle and difficult two
153
decades after this initial work, as the results are in accordance with chemical intuition we can
154
be confident in the ranking of the different pairs, and the absolute values are in any case less
155
important for the following discussion. From this tabulated data we can see that the weakest
156
step is CG (-4.36 kcal/mol), and the strongest is GG (-7.79). If we approximate the stacking
157
energy for complementary duplex DNA as the sum of the stacking energies for the two
base-158
steps, the weakest step remains CG-CG (-8.72 kcal/mol) and the strongest is GG-CC, with an
159
energy of -12.3 kcal/mol.
160
Based on the stacking energy of complementary pairs, it is possible to arrive at the
161
energetic cost to separate a given codon from its neighbours as a triplet of stacked base-pairs.
162
If we consider the duplex xGGCy-pGCCq (coding for GLY on strand 1, ALA on the
163
complementary strand, where x,y,p,q are bases from the adjacent codons), then the stacks
164
needed to find the triplet disproportionation energy Gτ are xG, Cy, pG, Cq. In order to select 165
x, y we randomly choose two amino acids from the set of phase one residues ADEGILPSTV,
166
and then randomly choose a codon for the given amino acid subject to the constraint that if a
167
codon beginning in G or ending in C (or both) is available in the genetic code, this codon is
168
preferred. The bases p, q are then selected as complementary to x, y. After sampling 106 amino
169
acid pairs, it is then possible to tabulate the average energy to partition into a triplet associated
170
with a given codon (Gτ). 171
If we assume that the DNA is subject to tension such that it must partition in some way,
172
and that the partitions must be somewhat evenly spread (here we arbitrarily assume two breaks
173
per five base-pairs) then we can present a relative free energy ΔGτ by comparing against the 174
alternative pairs of sites at which to break base-stacking. Combinatorics gives 1/2 (N2 – N)
9
such site combinations for a stretch of N steps, where N is 1 less than the number of base pairs.
176
Here 1/2 (N2 - N) = 6, leaving 5 site pairs for step breakage not including the pair which defines
177
a ‘Σ’ triplet. To get a probability, the comparison should be to a Boltzmann-weighted sum of
178
all alternative energies, i.e.:
179 1..5 / / /
e
e
( )
e
B B B i k T i G k T G G k Tp
180Tabulating this information for the 20 canonical amino acids, we can see a clear pattern
181
of reduced triplet disproportionation energy for the primordial ‘stage one’ amino acids (Table
182 1). 183
Table 1.
184 185The dramatic pattern evident in the tabulated partitioning energies is that stage one
186
amino acids overwhelmingly have relatively favourable free energies to partition into triplets
187
aligned to their codons. The exception to this pattern is interesting: Arginine (R) is not listed
188
in Wong and Bronskill’s 1979 tabulation of stage one amino acids (Wong and Bronskill, 1979),
189
possibly due to the large energetic cost needed to synthesize it from citrulline in modern
190
organisms (Ratnerand Petrack, 1953).
191
It has been advanced the CGN and AGN (where N = ‘anything’) codons which yield 192
Arginine in the modern genetic code previously coded for the chemically similar non-canonical 193
amino acid Ornithine (Jukes, 1973), and that the function of this codon was usurped in a 194
presumably dramatic evolutionary event when selection advantage was found in having access 195
to the more strongly basic Arginine molecule. The original list ADEGILPSTV contains no 196
10 range of folded proteins, and the replacement of Ornithine with Arginine a beneficial 198
evolutionary step in giving access to a stronger base. 199
Arginine stands out for a second reason: the DNA-binding recombinase RecA achieves
200
triplet disproportionation by cradling the negatively charged DNA in a large number of
201
positively charged R side-chains (and some K). Thus we should perhaps not be surprised if a
202
phase of biochemical evolution in which control of triplet disproportionation is important
203
should have some means to produce either Arginine or a similar moderately bulky basic
204
residues.
205
The weaker statement of this work, that the stage one part of the genetic code is
206
structured so as to support a minimisation of read-frame errors by physically favouring the
207
partition into aligned triplets under tension, is related to a known subtle and remarkable
208
property of the genetic code. This property is that its redundancy is structured almost-optimally
209
so as to support overlapping codes orthogonal to the primary code specifying amino acids
210
(Itzkovitz andAlon, 2007), allowing the evolution of sequence changes altering DNA structure
211
and interactions even within protein coding regions, without changing the coded protein. The
212
overall flexibility of the genetic code in allowing arbitrary steganographic codes is not however
213
sufficient to explain the strong pattern which we observe: Table 2 shows that codons for phase
214
one amino acids are significantly more able to encode this partitioning than those in phase 2.
215
We further observe that the residues advanced by Ikehara et al. (Ikehara et al. 2002) as forming
216
the minimal set for a functional proteome (marked ☥ in Table 2) are also those which partition
217
most naturally into triplets.
218
Table 2.
219
220
11 Spontaneous Triplet Disproportionation Under Tension, Amplified in the Presence of 222
Organic Cations 223
Beyond the pairwise hydrophobic and electrostatic interactions of base stacking (covered by
224
the classic calculation used to generate Tables 1 and 2) the potential importance of complex
225
entropic, structural and solvent effects makes it necessary to carry out a full atomistic molecular
226
dynamics investigation of DNA under tension. Given the expected importance of sequence
227
effects, simulations were run both with a low-entropy sequence of d[G12C12] (encoding 4
228
glycines and 4 prolines) and a sequence chosen to show strong triplet disproportionation based
229
on Table 1, d[(GGC)4(GAC)4], encoding four repeats each of the high-scoring amino acids Gly
230
and Asp on the first strand, then Val and Ala on the complementary strand (the GADV set of
231
(Ikehara et al. 2002). The DNA duplexes were stretched by an additional 100 Å from their
232
relaxed lengths, over a time period of 150 ns, giving a stretching rate of 0.029 Å ns-1 bp-1.
233
Because of the apparent importance of Arginine, based on Table 1 and on the RecA structure
234
(Chen et al., 2008), simulations were run both in NaCl and in a solution of Ac-Arg-NHMe Cl,
235
with the capped Arginine molecule replacing sodium as the positive counterion.
236
We find that for the GC-rich sequence encoding phase one amino acids, the
triplet-237
disproportionated Σ-phase of DNA is observed, with the strongest triplet formation taking
238
place in the presence of the terminus-capped Arginine residues (Ac-Arg-NHMe). Fig. 1 shows
239
a regular pattern of vertical bases with spacing 3 bp, over a large range of extensions. The
low-240
entropy sequence in the presence of Arginine shows some weak structure at high extensions,
241
due to exclusion effects which disfavour binding of cations to adjacent sites. In the
high-242
entropy sequence, some structure of period three is seen, even in the absence of Arginine,
243
however this is relatively weak (as suggested by the order1 𝑘𝐵𝑇 free energies of
244
disproportionation in Table 1).
245
Fig. 1
12
The triplet-disproportionated structures show the essential features of Σ-DNA (Fig. 2) as seen
247
in the RecA bound crystal structure: preserved Watson-Crick base-pairing, approximately
248
planar orientation of the bases (Fig. 3), and a large cavity every third base pair.
249
250
Fig. 2
251
Extending beyond approximately 3 Å/bp leads to breakup of the Σ phase and also to loss of
252
Watson-Crick hydrogen bonding, as the bases interdigitate with each other and hydrogen bond
253
to the backbone.
254
The average base-pair inclination in the high entropy sequence d[(GCC)4(GAC)4] in
255
the presence and absence of intercalators up to the extension point of 1.5 follow the same
256
pattern and remain flat (Fig. 3b,d,f) which indicates base-pair perpendicularity with respect to
257
the helix axis (Nordén et al., 1978; Edmondson and Johnson, 1986, Bosaeus et al., 2012). In
258
the presence of intercalators this trend continues after extension point of 1.5 but shows a sudden
259
drop for the duplexes in NaCl after a relative extension of 1.7. For the low entropy sequence
260
d[(G)12(C)12], the change of average inclination up to an extension of 1.5 is the same as for the
261
high entropy sequence. The bare sequence and the one in the presence of Arginine reach a
262
maximum inclination at a relative extension of 1.6-1.7 and drop afterwards (Fig. 3a,c) but in
263
the presence of EtBr a continuous increase is observed after extension 1.5, followed by a second
264
flat region after 1.6 (Fig. 3e). That average inclination tends to be small during DNA extension
265
for the high entropy sequence with or without organic cations is consistent with the results put
266
forward from experiment (Bosaeuset al. Current work) as suggesting Σ formation even in free
13 271
DISCUSSION
272 273
DNA behaviour under tension is affected by factors like the counterions (Vlassakis et al.,
274
2008), sequence (Riefet al., 1999) and temperature (Fu et al. 2010). Molecular combing results
275
show that DNA in its stretched form is not denatured, with a double-helix structure which is
276
characterized by a diameter of 1.2 nm (Maaloum et al., 2011). X-ray diffractions of stretched
277
cross-link films of a mixed sequence of DNA show gaps of ~8 Å (André et al., 2008), nearly
278
the same size as seen in the DNA-RecA complex. These experimental results suggest the
279
existence of a stretched form of DNA with preserved base-pair stacking.
280
In order to relate the physics of DNA stretching with its function in storing and copying
281
information, we have estimated the sequence dependence of the free energy cost in water at
282
moderate ionic strength to separate a given codon from its neighbours as a triplet of stacked
283
base-pairs, and found that although the aqueous solution environment does not strongly drive
284
triplet partitioning, that a distinct hierarchy of triplet formation energies exists with respect to
285
sequence features. The triplet formation energy estimates showed that sequences coding for
286
‘stage one’ amino acids hypothesized to have appeared early in evolution (plus Arginine) are
287
more likely than otherwise to partition into triplets at the codon boundaries when under tension.
288
In order to investigate this phenomenon we carried out pulling simulations of DNA duplexes
289
encoding stage one amino acids, in the presence of Arginine and also of Ethidium Bromide, as
290
well as control simulations using low-entropy sequences, and in aqueous conditions with
291
monatomic salt only.
292
In order to observe strong triplet disproportionation both a bulky organic cation (i.e.
293
Arginine or Ethidium) and a sequence selected from codons yielding phase-one amino acids
294
was required, with the combination of these two factors operating in a non-additive way to
295
produce a solution structure of stacked base-pair triplets. Overstretching the Σ-duplex led to
14
formation of interdigitated zipper DNA, stretching without cofactors or appropriate sequence
297
led to disordered but not fully denatured structure consistent with experiments (Balaeff et al., 298
2011; Bosaeuset al. Current work) and simulations (Konrad et al. 1996).
299
Ikehara and co-workers have shown that codons matching the pattern GNC (where N 300
signifies “anything”) probably constituted the original, minimal functional genetic code. These
301
authors argue based on multiple strands of reasoning that the amino acids GADV, translated
302
from these codons, constitute the unique minimal adequate set to generate functional globular
303
proteins (Ikehara et al. 2002). We argue that it is no coincidence that the same GNC codons
304
are those which drive maximal triplet disproportionation, allowing recombination and possibly
305
protein synthesis to operate without the sophisticated enzymatic machinery which exists today.
306
We hypothesize that a bootstrap process took place, with crude triplet disproportionation
307
facilitating recombination, driving accelerated evolution and leading to more sophisticated
308
protein-DNA interactions, in turn allowing expansion in stages of the genetic code.
309 310 311 312 313 314 315 Speculative box 316
We speculate that Ornithine (instead of Arginine) may play the role of triplet promoter 317
in some organisms, or have done so earlier in the evolutionary process. The usurpation 318
of Ornithine codons to instead signify Arginine may have led to a jump in the efficiency 319
of recombination and an evolutionary explosion. 320
15 322
Acknowledgements 323
This project was financially supported by the University of Luxembourg. Computer
324
simulations presented in this paper were carried out using the HPC facility of the University of
325
Luxembourg (Varrette et al., 2014). We thank Bengt Nordén for considerable guidance,
326
criticism and inspiration.
327
328
329
Financial support 330
This work was supported by the University of Luxembourg (grant number R-AGR-0136).
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22 Amirhossein Taghavi, Paul van der Schoot and Joshua T. Berryman
DNA partitions into triplets under tension….
23 Amirhossein Taghavi, Paul van der Schoot and Joshua T. Berryman
DNA partitions into triplets under tension….
24 Amirhossein Taghavi, Paul van der Schoot and Joshua T. Berryman
DNA partitions into triplets under tension….
25 Amirhossein Taghavi, Paul van der Schoot and Joshua T. Berryman
DNA partitions into triplets under tension….
26 Amirhossein Taghavi, Paul van der Schoot and Joshua T. Berryman
DNA partitions into triplets under tension….
27 Amirhossein Taghavi, Paul van der Schoot and Joshua T. Berryman
DNA partitions into triplets under tension….
Figure 1.
Kymographs of rise per bp-step under imposed whole- DNA extension. Triplet disproportionation is strongly evident in (b), while the strain is spread most evenly in (c). Presence of Arginine in a homogenous sequence (a) or presence of CG steps in the absence of Arginine (d) induce only weakly structured disproportionation.
Figure 2.
The ‘primordial’ sequence partitions under tension predominantly at the CG steps, forming triplets (a),
with Watson-Crick hydrogen bonding and planar base stacking preserved subject to some thermal disorder (a,b). Triplets are stabilised by one or two Arginines intercalating the stretched base steps (b,c) with non-specific binding that tends to place the charged end of the side-chain close to the phosphate, and partially or entirely excludes water from between the bases.
(c) is an axial view of the highlighted cavity in (b).
Figure 3.
28 Amirhossein Taghavi, Paul van der Schoot and Joshua T. Berryman
DNA partitions into triplets under tension….
Table 1.
Phase one amino acids (*,☥) tend to have (at least one) codon associated with them that partitions favourably at its boundaries. The most favourable partitioning is for the phase zero (DAGV) amino acids (☥). X indicates a stop codon, other letters are standard amino acid abbreviations. Energy units are kcal/mol.
Table 2.
